shapiroDonor {SPLINTER} | R Documentation

## shapiroDonor

### Description

Shapiro and Senapathy (1987) have developed a method to score the strength of a splice site based on percentages of each nucleotide at each position. Shapiro's score of donor site (range is from -3 [exon] to +7 [intron]) is : 100 * (t - min)/ (max - min), where t is the sum of percentages at positions -3 to +7, min is the sum of the lowest percentages at positions -3 to +7, and max is the sum of the highest percentages at positions -3 to +7.

### Usage

    shapiroDonor(reference_fasta, target_fasta)

### Arguments

`reference_fasta` | vector of strings or DNAStringSet of reference splice list
`target_fasta` | vector of strings or DNAStringSet of fasta to score

### Value

data.frame with Shapiro scores

### Author(s)

Diana Low

Diana Low

### See Also

http://www.softberry.com/spldb/SpliceDB.html

### Examples

    library(BSgenome.Mmusculus.UCSC.mm9)
    bsgenome <- BSgenome.Mmusculus.UCSC.mm9
    data_path<-system.file("extdata",package="SPLINTER")
    splice_data<-extractSpliceEvents(data=paste(data_path,"/skipped_exons.txt",sep=""))
    splice_sites<-extractSpliceSites(splice_data)
    donor.ss<-getSeq(bsgenome,splice_sites)
    sdonor<-shapiroDonor(donor.m,donor.ss)

[Package SPLINTER version 1.8.1 Index]